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This page was generated on 2023-05-10 10:04:42 -0000 (Wed, 10 May 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6211 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
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To the developers/maintainers of the SynExtend package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/SynExtend.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 2025/2194 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| SynExtend 1.13.0 (landing page) Nicholas Cooley
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: SynExtend |
| Version: 1.13.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SynExtend_1.13.0.tar.gz |
| StartedAt: 2023-05-10 06:40:55 -0000 (Wed, 10 May 2023) |
| EndedAt: 2023-05-10 06:44:46 -0000 (Wed, 10 May 2023) |
| EllapsedTime: 230.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: SynExtend.Rcheck |
| Warnings: 0 |
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### Running command:
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### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:SynExtend.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings SynExtend_1.13.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/SynExtend.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘SynExtend/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘SynExtend’ version ‘1.13.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘SynExtend’ can be installed ... OK
* used C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
predict.ProtWeaver 19.477 0.102 19.573
BuiltInEnsembles 17.143 0.253 17.391
BlockExpansion 12.179 0.372 12.558
gffToDataFrame 9.154 0.056 9.212
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘UsingSynExtend.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: 1 NOTE
See
‘/home/biocbuild/bbs-3.17-bioc/meat/SynExtend.Rcheck/00check.log’
for details.
SynExtend.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL SynExtend ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library’ * installing *source* package ‘SynExtend’ ... ** using staged installation ** libs using C compiler: ‘gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0’ gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c CDend.c -o CDend.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c CShuffle.c -o CShuffle.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c HungarianAlgo.c -o HungarianAlgo.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c MoranI.c -o MoranI.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c NucleotideCounts.c -o NucleotideCounts.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c R_init_synextend.c -o R_init_synextend.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c SEutils.c -o SEutils.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c XORRand.c -o XORRand.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c calcMIR2C.c -o calcMIR2C.o gcc -I"/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/lib/R/include" -DNDEBUG -I/usr/local/include -fopenmp -fPIC -g -O2 -c dendrapply.c -o dendrapply.o gcc -shared -L/usr/local/lib -o SynExtend.so CDend.o CShuffle.o HungarianAlgo.o MoranI.o NucleotideCounts.o R_init_synextend.o SEutils.o XORRand.o calcMIR2C.o dendrapply.o -fopenmp installing to /home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/00LOCK-SynExtend/00new/SynExtend/libs ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** checking absolute paths in shared objects and dynamic libraries ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (SynExtend)
SynExtend.Rcheck/SynExtend-Ex.timings
| name | user | system | elapsed | |
| BlastSeqs | 0 | 0 | 0 | |
| BlockExpansion | 12.179 | 0.372 | 12.558 | |
| BlockReconciliation | 0.211 | 0.004 | 0.215 | |
| BuiltInEnsembles | 17.143 | 0.253 | 17.391 | |
| CIDist_NullDist | 0.002 | 0.000 | 0.002 | |
| DPhyloStatistic | 0.044 | 0.000 | 0.045 | |
| DisjointSet | 0.025 | 0.003 | 0.029 | |
| Endosymbionts_GeneCalls | 0.013 | 0.000 | 0.014 | |
| Endosymbionts_LinkedFeatures | 0.015 | 0.000 | 0.015 | |
| Endosymbionts_Pairs01 | 0.014 | 0.000 | 0.015 | |
| Endosymbionts_Pairs02 | 0.011 | 0.004 | 0.014 | |
| Endosymbionts_Pairs03 | 0.011 | 0.004 | 0.015 | |
| Endosymbionts_Sets | 0.002 | 0.000 | 0.002 | |
| Endosymbionts_Synteny | 0.002 | 0.000 | 0.002 | |
| EstimRearrScen | 1.729 | 0.052 | 1.782 | |
| ExampleStreptomycesData | 1.811 | 0.026 | 1.835 | |
| ExtractBy | 0.243 | 0.008 | 0.251 | |
| FindSets | 0.002 | 0.000 | 0.002 | |
| Generic | 0.003 | 0.000 | 0.003 | |
| MoransI | 0.001 | 0.000 | 0.001 | |
| NucleotideOverlap | 0.327 | 0.004 | 0.330 | |
| PairSummaries | 2.685 | 0.008 | 2.693 | |
| PhyloDistance-CI | 0.005 | 0.000 | 0.006 | |
| PhyloDistance-JRF | 0.004 | 0.000 | 0.004 | |
| PhyloDistance-KF | 0.002 | 0.000 | 0.002 | |
| PhyloDistance-RF | 0.002 | 0.000 | 0.002 | |
| PhyloDistance | 0.004 | 0.000 | 0.005 | |
| ProtWeaver | 0.003 | 0.000 | 0.004 | |
| ProtWeb | 0.699 | 0.002 | 0.700 | |
| SelectByK | 0.122 | 0.000 | 0.122 | |
| SequenceSimilarity | 0.086 | 0.000 | 0.088 | |
| SubSetPairs | 0.064 | 0.000 | 0.063 | |
| SuperTree | 3.368 | 0.068 | 3.437 | |
| SuperTreeEx | 0.091 | 0.000 | 0.091 | |
| dendrapply | 0.156 | 0.004 | 0.161 | |
| gffToDataFrame | 9.154 | 0.056 | 9.212 | |
| plot.ProtWeb | 2.574 | 0.008 | 2.583 | |
| predict.ProtWeaver | 19.477 | 0.102 | 19.573 | |
| simMat | 0.014 | 0.000 | 0.014 | |